Variant report

Variant	rs6446208
Chromosome Location	chr3:50687825-50687826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50643169..50645123-chr3:50685747..50687888,2	MCF-7	breast:
2	chr3:50674743..50676544-chr3:50686254..50688455,2	K562	blood:
3	chr3:50652070..50655267-chr3:50687224..50691419,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1013233	0.88[AFR][1000 genomes]
rs1077215	0.95[ASN][1000 genomes]
rs12486143	0.86[AMR][1000 genomes]
rs12486717	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487817	0.87[AMR][1000 genomes]
rs12489607	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12491440	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12491812	0.89[AMR][1000 genomes]
rs12492093	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492540	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492982	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494094	0.81[AMR][1000 genomes]
rs12494326	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12495399	0.85[ASN][1000 genomes]
rs1385025	0.86[AFR][1000 genomes]
rs17050991	0.89[AMR][1000 genomes]
rs17050995	0.86[AMR][1000 genomes]
rs17051000	0.81[AMR][1000 genomes]
rs17051043	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17051045	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17051403	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872184	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894459	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1971976	0.84[AFR][1000 genomes]
rs2035484	0.91[ASN][1000 genomes]
rs2076927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170840	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227292	0.86[ASN][1000 genomes]
rs2227293	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2239750	0.86[ASN][1000 genomes]
rs2239751	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239753	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34848480	0.86[AFR][1000 genomes]
rs3749265	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3752449	0.86[ASN][1000 genomes]
rs375544	0.84[AFR][1000 genomes]
rs3792323	0.91[ASN][1000 genomes]
rs3792325	0.82[AFR][1000 genomes]
rs3792328	0.84[AFR][1000 genomes]
rs3804632	0.83[AFR][1000 genomes]
rs3943212	0.84[AFR][1000 genomes]
rs396302	0.83[AFR][1000 genomes]
rs443436	0.86[AFR][1000 genomes]
rs4476497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs448028	0.83[AFR][1000 genomes]
rs4688705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688707	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4688709	0.86[ASN][1000 genomes]
rs4688710	0.81[AMR][1000 genomes]
rs4688713	0.86[AMR][1000 genomes]
rs56170012	0.84[AMR][1000 genomes]
rs56856095	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57910827	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58427389	0.94[ASN][1000 genomes]
rs58529408	0.91[ASN][1000 genomes]
rs59036236	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60552073	0.81[AMR][1000 genomes]
rs60552386	0.81[ASN][1000 genomes]
rs60877431	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61193866	0.89[AMR][1000 genomes]
rs61316441	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61574029	0.90[AMR][1000 genomes]
rs61613532	0.90[AMR][1000 genomes]
rs616589	0.84[AFR][1000 genomes]
rs616689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446212	0.84[AFR][1000 genomes]
rs650655	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6766638	0.87[AMR][1000 genomes]
rs6771348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6783922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794155	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs728901	0.88[AFR][1000 genomes]
rs728902	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72938758	0.90[AMR][1000 genomes]
rs72942785	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72942794	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72944726	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944730	0.91[ASN][1000 genomes]
rs73835531	0.86[AMR][1000 genomes]
rs743753	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs745356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751851	0.86[AFR][1000 genomes]
rs762889	0.86[ASN][1000 genomes]
rs808148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs808149	0.88[AFR][1000 genomes]
rs813243	0.81[AFR][1000 genomes]
rs876103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs876104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs876105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs900735	0.88[AFR][1000 genomes]
rs9682401	0.88[AFR][1000 genomes]
rs9868889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9879397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
2	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:50670200-50689000	Weak transcription	K562	blood
4	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
5	chr3:50672400-50688000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:50675800-50688000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:50676000-50688200	Strong transcription	Primary T cells from cord blood	blood
8	chr3:50676000-50689200	Strong transcription	Fetal Intestine Small	intestine
9	chr3:50676400-50688000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:50676400-50688000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:50676400-50688800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:50676600-50688200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:50676800-50688000	Strong transcription	Esophagus	oesophagus
14	chr3:50677400-50692200	Weak transcription	NHDF-Ad	bronchial
15	chr3:50680200-50689200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:50681000-50689200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:50682600-50689000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:50684400-50688800	Weak transcription	NHLF	lung
19	chr3:50684600-50688000	Enhancers	Brain Angular Gyrus	brain
20	chr3:50684600-50688000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:50684800-50688000	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:50684800-50688000	Enhancers	Brain Hippocampus Middle	brain
23	chr3:50684800-50688000	Enhancers	Brain Substantia Nigra	brain
24	chr3:50685000-50688200	Enhancers	Brain Anterior Caudate	brain
25	chr3:50685000-50688400	Weak transcription	HepG2	liver
26	chr3:50685000-50688600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:50685000-50690000	Enhancers	Fetal Brain Female	brain
28	chr3:50685200-50689000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:50685200-50689200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:50685200-50691600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:50685200-50692800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:50685400-50688200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:50685400-50689200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:50685400-50689800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:50685400-50690200	Enhancers	Fetal Brain Male	brain
36	chr3:50685400-50693000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:50685400-50693000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:50685800-50692400	Weak transcription	Osteobl	bone
39	chr3:50685800-50703800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:50686000-50688000	Genic enhancers	Fetal Stomach	stomach
41	chr3:50686000-50688600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:50686000-50690400	Enhancers	Left Ventricle	heart
43	chr3:50686000-50690400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:50686200-50688000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:50686200-50688000	Enhancers	Ovary	ovary
46	chr3:50686200-50689000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:50686400-50692600	Weak transcription	Fetal Thymus	thymus
48	chr3:50686600-50688200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:50686600-50688600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:50686600-50690600	Weak transcription	Adipose Nuclei	Adipose

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